Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation - PubMed (original) (raw)
René L Warren 1, Ewan A Gibb 1, Benjamin P Vandervalk 1, Hamid Mohamadi 1, Justin Chu 1, Anthony Raymond 1, Stephen Pleasance 1, Robin Coope 1, Mark R Wildung 2, Carol E Ritland 3, Jean Bousquet 4, Steven J M Jones 5, Joerg Bohlmann 6, Inanç Birol 7
Affiliations
- PMID: 26645680
- PMCID: PMC4758241
- DOI: 10.1093/gbe/evv244
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation
Shaun D Jackman et al. Genome Biol Evol. 2015.
Abstract
The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors hundreds of mitochondria and plastids. Hence, assembly of the 123-kb plastid and 5.9-Mb mitochondrial genomes were accomplished by analyzing data sets primarily representing low coverage of the nuclear genome. The assembled organellar genomes were annotated for their coding genes, ribosomal RNA, and transfer RNA. Transcript abundances of the mitochondrial genes were quantified in three developmental tissues and five mature tissues using data from RNA-seq experiments. C-to-U RNA editing was observed in the majority of mitochondrial genes, and in four genes, editing events were noted to modify ACG codons to create cryptic AUG start codons. The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data.
Keywords: ABySS; genome assembly; gymnosperms; organelle; sequencing; white spruce.
© The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Figures
Fig. 1.—
The complete plastid genome of white spruce. The PG29 white spruce chloroplast genome was annotated using MAKER and plotted using OrganellarGenomeDRAW (Lohse et al. 2007). The inner gray track depicts the G+C content of the genome.
Fig. 2.—
Relative order and size of genes on the scaffolds of the white spruce mitochondrial genome. Each box is proportional to the size of the gene including introns, except that genes smaller than 200 bp are shown as 200 bp. The space between genes is not to scale. An asterisk indicates that the gene name is truncated. Only scaffolds that harbor annotated genes are shown.
Fig. 3.—
Gene content of the white spruce mitochondrial genome, grouped by gene family. Each box is proportional to the size of the gene including introns. The color of each gene is unique within its gene family.
Fig. 4.—
Repetitive sequence content of the white spruce mitochondrial genome, annotated using RepeatMasker and RepeatModeler.
Fig. 5.—
Heatmap of the transcript abundance of mitochondrial protein-coding genes of white spruce. Each column is a tissue sample. Each row is a gene. Each cell represents the transcript abundance of one gene in one sample. The color scale is log10(TPM+1), where TPM is transcripts per million as measured by Salmon (Patro et al. 2014).
Fig. 6.—
Heatmap of the transcript abundance of mitochondrial protein-coding genes of white spruce, including ORFs. Each column is a tissue sample. Each row is a gene. Each cell represents the transcript abundance of one gene in one sample. The color scale is log10(TPM+1), where TPM is transcripts per million as measured by Salmon (Patro et al. 2014).
References
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